Commit a8246ca8 authored by Tom Harrop's avatar Tom Harrop
Browse files

add pod5 

(cherry picked from commit aa2b3813)
parent 21e7a222

lib/galaxy/config/sample/datatypes_conf.xml.sample

+2 −0
Original line number Diff line number Diff line
@@ -361,6 +361,7 @@ 
    <datatype extension="fast5.tar.gz" type="galaxy.datatypes.binary:Fast5ArchiveGz" display_in_upload="true"/>

    <datatype extension="fast5.tar.bz2" type="galaxy.datatypes.binary:Fast5ArchiveBz2" display_in_upload="true"/>

    <datatype extension="fast5.tar.xz" type="galaxy.datatypes.binary:Fast5ArchiveXz" display_in_upload="true"/>

    <datatype extension="pod5" type="galaxy.datatypes.binary:Pod5" display_in_upload="true"/>

    <datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>

    <datatype extension="percin" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>

    <datatype extension="percout" type="galaxy.datatypes.xml:GenericXml" subclass="true"/>
@@ -1079,6 +1080,7 @@ 
    <sniffer type="galaxy.datatypes.binary:Fast5ArchiveXz"/>

    <sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2"/>

    <sniffer type="galaxy.datatypes.binary:Fast5Archive"/>

    <sniffer type="galaxy.datatypes.binary:Pod5"/>

    <sniffer type="galaxy.datatypes.binary:Meryldb" />

    <sniffer type="galaxy.datatypes.binary:Bref3" />

    <sniffer type="galaxy.datatypes.binary:PostgresqlArchive"/>

lib/galaxy/datatypes/binary.py

+29 −0
Original line number Diff line number Diff line
@@ -3759,6 +3759,35 @@ class Fast5ArchiveBz2(Fast5Archive): 
        return Fast5Archive.sniff(self, filename)





class Pod5(Binary):

    """

    Class describing a Pod5 file



    >>> from galaxy.datatypes.sniff import get_test_fname

    >>> fname = get_test_fname('test.pod5')

    >>> Pod5().sniff(fname)

    True

    """



    file_ext = "pod5"



    def sniff(self, filename: str) -> bool:

        expected_signature = bytes(

            [0x8B, 0x50, 0x4F, 0x44, 0x0D, 0x0A, 0x1A, 0x0A]

        )

        try:

            with open(filename, "rb") as f:

                first_8_bytes = f.read(8)

                f.seek(-8, 2)

                last_8_bytes = f.read(8)

                return (

                    first_8_bytes == expected_signature

                    and last_8_bytes == expected_signature

                )

        except Exception:

            return False





class SearchGuiArchive(CompressedArchive):

    """Class describing a SearchGUI archive"""

lib/galaxy/datatypes/test/test.pod5

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